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Choi YJ, Kim Y, Park HJ, Kim D, Lee H, Kim YA, Lee KA. Development of a multiplex droplet digital PCR method for detection and monitoring of Mycobacterium tuberculosis and drug-resistant tuberculosis. Ann Clin Microbiol Antimicrob 2024; 23:29. [PMID: 38581051 PMCID: PMC10998390 DOI: 10.1186/s12941-024-00687-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Accepted: 03/21/2024] [Indexed: 04/07/2024] Open
Abstract
BACKGROUND The prevalence of multidrug-resistant tuberculosis (MDR-TB) among Korean tuberculosis patients is about 4.1%, which is higher than the OECD average of 2.6%. Inadequate drug use and poor patient compliance increase MDR-TB prevalence through selective pressure. Therefore, prompt detection of drug resistance in tuberculosis patients at the time of diagnosis and quantitative monitoring of these resistant strains during treatment are crucial. METHODS A multiplex droplet digital PCR (ddPCR) assay was developed and assessed using DNA material of nine Mycobacterium tuberculosis strains with known mutation status that were purchased from the Korean National Tuberculosis Association. We collected a total of 18 MDR-TB residual samples referred for PCR analysis. Total DNA was extracted from the samples and subjected to the quadruplex ddPCR assay. Their results were compared to those of known resistance phenotypes. RESULTS The analytical sensitivity and specificity of the multiplex ddPCR assay for detecting INH, RIF, EMB, FQ, and SM resistance-causing mutations ranged from 71.43 to 100% and 94.12-100%, respectively. Follow-up sample results showed that the quadruplex ddPCR assay was sensitive enough to detect IS6110 and other mutations even after onset of treatment. CONCLUSIONS We developed a sensitive and accurate multiplex ddPCR assay that can detect the presence of tuberculosis quantitatively and resistance-conveying mutations concurrently. This tool could aid clinicians in the diagnosis and treatment monitoring of tuberculosis.
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Affiliation(s)
- Yu Jeong Choi
- Department of Laboratory Medicine, Gangnam Severance Hospital, Yonsei University College of Medicine, 211, Eonju-ro, Gangnam-gu, Seoul, 06273, Korea
| | - Yoonjung Kim
- Department of Laboratory Medicine, Gangnam Severance Hospital, Yonsei University College of Medicine, 211, Eonju-ro, Gangnam-gu, Seoul, 06273, Korea
| | - Hye Jung Park
- Department of Internal Medicine, Yonsei University College of Medicine, Seoul, Korea
| | - Dokyun Kim
- Department of Laboratory Medicine, Gangnam Severance Hospital, Yonsei University College of Medicine, 211, Eonju-ro, Gangnam-gu, Seoul, 06273, Korea
| | - Hyukmin Lee
- Department of Laboratory Medicine, Gangnam Severance Hospital, Yonsei University College of Medicine, 211, Eonju-ro, Gangnam-gu, Seoul, 06273, Korea
| | - Young Ah Kim
- Department of Laboratory Medicine, National Health Insurance Service Ilsan Hospital, Goyang, Korea
| | - Kyung-A Lee
- Department of Laboratory Medicine, Gangnam Severance Hospital, Yonsei University College of Medicine, 211, Eonju-ro, Gangnam-gu, Seoul, 06273, Korea.
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2
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Systematic review and meta-analysis: Diagnostic performance of DNA alterations in pancreatic juice for the detection of pancreatic cancer. Pancreatology 2022; 22:973-986. [PMID: 35864067 DOI: 10.1016/j.pan.2022.06.260] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/22/2022] [Revised: 06/20/2022] [Accepted: 06/22/2022] [Indexed: 12/11/2022]
Abstract
BACKGROUND AND AIMS Pancreatic cancer has a dismal prognosis. So far, imaging has been proven incapable of establishing an early enough diagnosis. Thus, biomarkers are urgently needed for early detection and improved survival. Our aim was to evaluate the pooled diagnostic performance of DNA alterations in pancreatic juice. METHODS A systematic literature search was performed in EMBASE, MEDLINE Ovid, Cochrane CENTRAL and Web of Science for studies concerning the diagnostic performance of DNA alterations in pancreatic juice to differentiate patients with high-grade dysplasia or pancreatic cancer from controls. Study quality was assessed using QUADAS-2. The pooled prevalence, sensitivity, specificity and diagnostic odds ratio were calculated. RESULTS Studies mostly concerned cell-free DNA mutations (32 studies: 939 cases, 1678 controls) and methylation patterns (14 studies: 579 cases, 467 controls). KRAS, TP53, CDKN2A, GNAS and SMAD4 mutations were evaluated most. Of these, TP53 had the highest diagnostic performance with a pooled sensitivity of 42% (95% CI: 31-54%), specificity of 98% (95%-CI: 92%-100%) and diagnostic odds ratio of 36 (95% CI: 9-133). Of DNA methylation patterns, hypermethylation of CDKN2A, NPTX2 and ppENK were studied most. Hypermethylation of NPTX2 performed best with a sensitivity of 39-70% and specificity of 94-100% for distinguishing pancreatic cancer from controls. CONCLUSIONS This meta-analysis shows that, in pancreatic juice, the presence of distinct DNA mutations (TP53, SMAD4 or CDKN2A) and NPTX2 hypermethylation have a high specificity (close to 100%) for the presence of high-grade dysplasia or pancreatic cancer. However, the sensitivity of these DNA alterations is poor to moderate, yet may increase if they are combined in a panel.
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Tan LL, Loganathan N, Agarwalla S, Yang C, Yuan W, Zeng J, Wu R, Wang W, Duraiswamy S. Current commercial dPCR platforms: technology and market review. Crit Rev Biotechnol 2022; 43:433-464. [PMID: 35291902 DOI: 10.1080/07388551.2022.2037503] [Citation(s) in RCA: 40] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Digital polymerase chain reaction (dPCR) technology has provided a new technique for molecular diagnostics, with superior advantages, such as higher sensitivity, precision, and specificity over quantitative real-time PCRs (qPCR). Eight companies have offered commercial dPCR instruments: Fluidigm Corporation, Bio-Rad, RainDance Technologies, Life Technologies, Qiagen, JN MedSys Clarity, Optolane, and Stilla Technologies Naica. This paper discusses the working principle of each offered dPCR device and compares the associated: technical aspects, usability, costs, and current applications of each dPCR device. Lastly, up-and-coming dPCR technologies are also presented, as anticipation of how the dPCR device landscape may likely morph in the next few years.
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Affiliation(s)
- Li Ling Tan
- Singapore Institute of Manufacturing Technology, Singapore, Singapore.,Materials Science and Engineering School, Nanyang Technological University, Singapore, Singapore
| | - Nitin Loganathan
- Singapore Institute of Manufacturing Technology, Singapore, Singapore
| | - Sushama Agarwalla
- Department of Chemical Engineering, Indian Institute of Technology Hyderabad, Hyderabad, India
| | - Chun Yang
- Mechanical and Aerospace Engineering School, Nanyang Technological University, Singapore, Singapore
| | - Weiyong Yuan
- Faculty of Materials & Energy, Institute for Clean Energy and Advanced Materials, Southwest University, Chongqing, China.,Chongqing Key Laboratory for Advanced Materials and Technologies of Clean Energies, Chongqing, China
| | - Jasmine Zeng
- Singapore Institute of Manufacturing Technology, Singapore, Singapore
| | - Ruige Wu
- Singapore Institute of Manufacturing Technology, Singapore, Singapore
| | - Wei Wang
- Singapore Institute of Manufacturing Technology, Singapore, Singapore
| | - Suhanya Duraiswamy
- Department of Chemical Engineering, Indian Institute of Technology Hyderabad, Hyderabad, India
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4
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Mishra S, Jeon J, Kang JK, Song SH, Kim TY, Ban C, Choi H, Kim Y, Kim M, Park JW. Direct Detection of Low Abundance Genes of Single Point Mutation. NANO LETTERS 2021; 21:9061-9068. [PMID: 34672610 DOI: 10.1021/acs.nanolett.1c02728] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Cell-free DNA (cfDNA) analysis, specifically circulating tumor DNA (ctDNA) analysis, provides enormous opportunities for noninvasive early assessment of cancers. To date, PCR-based methods have led this field. However, the limited sensitivity/specificity of PCR-based methods necessitates the search for new methods. Here, we describe a direct approach to detect KRAS G12D mutated genes in clinical ctDNA samples with the utmost LOD and sensitivity/specificity. In this study, MutS protein was immobilized on the tip of an atomic force microscope (AFM), and the protein sensed the mismatched sites of the duplex formed between the capture probe on the surface and mutated DNA. A noteworthy LOD (3 copies, 0.006% allele frequency) was achieved, along with superb sensitivity/specificity (100%/100%). These observations demonstrate that force-based AFM, in combination with the protein found in nature and properly designed capture probes/blockers, represents an exciting new avenue for ctDNA analysis.
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Affiliation(s)
- Sourav Mishra
- Department of Chemistry, Pohang University of Science and Technology, 77 Cheongam-Ro, Nam-Gu, Pohang 37673, Republic of Korea
| | - Jinseong Jeon
- Department of Chemistry, Pohang University of Science and Technology, 77 Cheongam-Ro, Nam-Gu, Pohang 37673, Republic of Korea
| | - Jun-Kyu Kang
- Cancer Genomics Research Laboratory, Cancer Research Institute, Seoul National University, Seoul 03080, Republic of Korea
- Department of Molecular Medicine and Biopharmaceutical Sciences, Graduate School of Convergence Science and Technology, Seoul National University, Seoul 03080, Republic of Korea
| | - Sang-Hyun Song
- Cancer Genomics Research Laboratory, Cancer Research Institute, Seoul National University, Seoul 03080, Republic of Korea
- Department of Molecular Medicine and Biopharmaceutical Sciences, Graduate School of Convergence Science and Technology, Seoul National University, Seoul 03080, Republic of Korea
| | - Tae-You Kim
- Cancer Genomics Research Laboratory, Cancer Research Institute, Seoul National University, Seoul 03080, Republic of Korea
- Department of Molecular Medicine and Biopharmaceutical Sciences, Graduate School of Convergence Science and Technology, Seoul National University, Seoul 03080, Republic of Korea
- Department of Internal Medicine, Seoul National University Hospital, Seoul 03080, Republic of Korea
| | - Changill Ban
- Department of Chemistry, Pohang University of Science and Technology, 77 Cheongam-Ro, Nam-Gu, Pohang 37673, Republic of Korea
- Institute of Convergence Science, Yonsei University, 50 Yonsei-ro, Seodaemun-gu, Seoul 03722, Republic of Korea
| | - Hayoung Choi
- Catholic Genetic Laboratory Center, Seoul St. Mary's Hospital, College of Medicine, The Catholic University of Korea, Seoul 06591, Republic of Korea
| | - Yonggoo Kim
- Catholic Genetic Laboratory Center, Seoul St. Mary's Hospital, College of Medicine, The Catholic University of Korea, Seoul 06591, Republic of Korea
- Department of Laboratory Medicine, College of Medicine, The Catholic University of Korea, Seoul 06591, Republic of Korea
| | - Myungshin Kim
- Catholic Genetic Laboratory Center, Seoul St. Mary's Hospital, College of Medicine, The Catholic University of Korea, Seoul 06591, Republic of Korea
- Department of Laboratory Medicine, College of Medicine, The Catholic University of Korea, Seoul 06591, Republic of Korea
| | - Joon Won Park
- Department of Chemistry, Pohang University of Science and Technology, 77 Cheongam-Ro, Nam-Gu, Pohang 37673, Republic of Korea
- Institute of Convergence Science, Yonsei University, 50 Yonsei-ro, Seodaemun-gu, Seoul 03722, Republic of Korea
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Label-free enrichment of rare unconventional circulating neoplastic cells using a microfluidic dielectrophoretic sorting device. Commun Biol 2021; 4:1130. [PMID: 34561533 PMCID: PMC8463600 DOI: 10.1038/s42003-021-02651-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Accepted: 09/08/2021] [Indexed: 02/08/2023] Open
Abstract
Cellular circulating biomarkers from the primary tumor such as circulating tumor cells (CTCs) and circulating hybrid cells (CHCs) have been described to harbor tumor-like phenotype and genotype. CHCs are present in higher numbers than CTCs supporting their translational potential. Methods for isolation of CHCs do not exist and are restricted to low-throughput, time consuming, and biased methodologies. We report the development of a label-free dielectrophoretic microfluidic platform facilitating enrichment of CHCs in a high-throughput and rapid fashion by depleting healthy peripheral blood mononuclear cells (PBMCs). We demonstrated up to 96.5% depletion of PBMCs resulting in 18.6-fold enrichment of cancer cells. In PBMCs from pancreatic adenocarcinoma patients, the platform enriched neoplastic cells identified by their KRAS mutant status using droplet digital PCR with one hour of processing. Enrichment was achieved in 75% of the clinical samples analyzed, establishing this approach as a promising way to non-invasively analyze tumor cells from patients.
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6
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Bidshahri R, Fakhfakh K, McNeil K, Won JR, Wolber R, Hughesman C, Haynes C. Analysis of
KRAS
G12
/
G13
in colorectal cancer using an economical digital
PCR
assay that unequivocally differentiates missense and synonymous alleles. CAN J CHEM ENG 2021. [DOI: 10.1002/cjce.24243] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Roza Bidshahri
- Michael Smith Laboratories University of British Columbia Vancouver British Columbia Canada
- Biomedical Engineering Program University of British Columbia Vancouver British Columbia Canada
| | - Kareem Fakhfakh
- Michael Smith Laboratories University of British Columbia Vancouver British Columbia Canada
- Department of Chemical and Biological Engineering University of British Columbia Vancouver British Columbia Canada
| | - Kelly McNeil
- Department of Genetics and Molecular Diagnostics British Columbia Cancer Agency Vancouver British Columbia Canada
| | - Jennifer R. Won
- Canadian Immunohistochemistry Quality Control, Department of Pathology and Laboratory Medicine University of British Columbia Vancouver British Columbia Canada
| | - Robert Wolber
- Canadian Immunohistochemistry Quality Control, Department of Pathology and Laboratory Medicine University of British Columbia Vancouver British Columbia Canada
- Department of Pathology Lion's Gate Hospital North Vancouver British Columbia Canada
| | - Curtis Hughesman
- Cancer Genetics and Genomics Lab British Columbia Cancer Agency Vancouver British Columbia Canada
| | - Charles Haynes
- Michael Smith Laboratories University of British Columbia Vancouver British Columbia Canada
- Biomedical Engineering Program University of British Columbia Vancouver British Columbia Canada
- Department of Chemical and Biological Engineering University of British Columbia Vancouver British Columbia Canada
- Genome Sciences and Technology Program Vancouver British Columbia Canada
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7
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A Quantitative Paradigm for Decision-Making in Precision Oncology. Trends Cancer 2021; 7:293-300. [PMID: 33637444 DOI: 10.1016/j.trecan.2021.01.006] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Revised: 01/16/2021] [Accepted: 01/20/2021] [Indexed: 11/24/2022]
Abstract
The complexity and variability of cancer progression necessitate a quantitative paradigm for therapeutic decision-making that is dynamic, personalized, and capable of identifying optimal treatment strategies for individual patients under substantial uncertainty. Here, we discuss the core components and challenges of such an approach and highlight the need for comprehensive longitudinal clinical and molecular data integration in its development. We describe the complementary and varied roles of mathematical modeling and machine learning in constructing dynamic optimal cancer treatment strategies and highlight the potential of reinforcement learning approaches in this endeavor.
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8
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Duong K, Ou J, Li Z, Lv Z, Dong H, Hu T, Zhang Y, Hanna A, Gordon S, Crynen G, Head SR, Ordoukhanian P, Wang Y. Increased sensitivity using real-time dPCR for detection of SARS-CoV-2. Biotechniques 2021; 70:7-20. [PMID: 33222514 PMCID: PMC7888512 DOI: 10.2144/btn-2020-0133] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2020] [Accepted: 10/15/2020] [Indexed: 02/06/2023] Open
Abstract
A real-time dPCR system was developed to improve the sensitivity, specificity and quantification accuracy of end point dPCR. We compared three technologies - real-time qPCR, end point dPCR and real-time dPCR - in the context of SARS-CoV-2. Some improvement in limit of detection was obtained with end point dPCR compared with real-time qPCR, and the limit of detection was further improved with the newly developed real-time dPCR technology through removal of false-positive signals. Real-time dPCR showed increased linear dynamic range compared with end point dPCR based on quantitation from amplification curves. Real-time dPCR can improve the performance of TaqMan assays beyond real-time qPCR and end point dPCR with better sensitivity and specificity, absolute quantification and a wider linear range of detection.
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Affiliation(s)
- Kyra Duong
- Gnomegen, 6440 Lusk Blvd, D207, San Diego, CA 92121, USA
| | - Jiajia Ou
- QuestGenomics, 12 E. Mozhou Rd, U-Park, Rm P308, Jiangning, Nanjing, Jiangsu, PR China
| | - Zhaoliang Li
- QuestGenomics, 12 E. Mozhou Rd, U-Park, Rm P308, Jiangning, Nanjing, Jiangsu, PR China
| | - Zhaoqing Lv
- QuestGenomics, 12 E. Mozhou Rd, U-Park, Rm P308, Jiangning, Nanjing, Jiangsu, PR China
| | - Hao Dong
- QuestGenomics, 12 E. Mozhou Rd, U-Park, Rm P308, Jiangning, Nanjing, Jiangsu, PR China
| | - Tao Hu
- QuestGenomics, 12 E. Mozhou Rd, U-Park, Rm P308, Jiangning, Nanjing, Jiangsu, PR China
| | - Yunyun Zhang
- QuestGenomics, 12 E. Mozhou Rd, U-Park, Rm P308, Jiangning, Nanjing, Jiangsu, PR China
| | - Ava Hanna
- Gnomegen, 6440 Lusk Blvd, D207, San Diego, CA 92121, USA
| | - Skyler Gordon
- Genomics Core Facility, Scripps Research, 10550 N Torrey Pines Road, La Jolla, CA, USA
| | - Gogce Crynen
- Bioinformatics Core Facility, Scripps Research, 120 Scripps Way, Jupiter, FL 33458, USA
| | - Steven R Head
- Genomics Core Facility, Scripps Research, 10550 N Torrey Pines Road, La Jolla, CA, USA
| | - Phillip Ordoukhanian
- Genomics Core Facility, Scripps Research, 10550 N Torrey Pines Road, La Jolla, CA, USA
| | - Yan Wang
- Gnomegen, 6440 Lusk Blvd, D207, San Diego, CA 92121, USA
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9
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Accurate, rapid and low-cost diagnosis of Mycoplasma pneumoniae via fast narrow-thermal-cycling denaturation bubble-mediated strand exchange amplification. Anal Bioanal Chem 2020; 412:8391-8399. [PMID: 33040157 PMCID: PMC7548028 DOI: 10.1007/s00216-020-02977-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Revised: 09/23/2020] [Accepted: 09/26/2020] [Indexed: 12/12/2022]
Abstract
Mycoplasma pneumoniae is a strong infectious pathogen that may cause severe respiratory infections. Since this pathogen may possess a latent period after infection, which sometimes leads to misdiagnosis by traditional diagnosis methods, the establishment of a rapid and sensitive diagnostic method is crucial for transmission prevention and timely treatment. Herein, a novel detection method was established for M. pneumoniae detection. The method, which improves upon a denaturation bubble-mediated strand exchange amplification (SEA) that we developed in 2016, is called accelerated SEA (ASEA). The established ASEA achieved detection of 1% M. pneumoniae genomic DNA in a DNA mixture from multiple pathogens, and the limit of detection (LOD) of ASEA was as low as 1.0 × 10-17 M (approximately 6.0 × 103 copies/mL). Considering that the threshold of an asymptomatic carriage is normally recommended as 1.0 × 104 copies/mL, this method was able to satisfy the requirement for practical diagnosis of M. pneumoniae. Moreover, the detection process was finished within 20.4 min, significantly shorter than real-time PCR and SEA. Furthermore, ASEA exhibited excellent performance in clinical specimen analysis, with sensitivity and specificity of 96.2% and 100%, respectively, compared with the "gold standard" real-time PCR. More importantly, similar to real-time PCR, ASEA requires only one pair of primers and ordinary commercial polymerase, and can be carried out using a conventional fluorescence real-time PCR instrument, which makes this method low-cost and easy to accomplish. Therefore, ASEA has the potential for wide use in the rapid detection of M. pneumoniae or other pathogens in large numbers of specimens. Graphical abstract.
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10
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Garcia-Cordero JL, Maerkl SJ. Microfluidic systems for cancer diagnostics. Curr Opin Biotechnol 2020; 65:37-44. [DOI: 10.1016/j.copbio.2019.11.022] [Citation(s) in RCA: 46] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2019] [Revised: 11/22/2019] [Accepted: 11/25/2019] [Indexed: 12/12/2022]
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11
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A novel approach for tuberculosis diagnosis using exosomal DNA and droplet digital PCR. Clin Microbiol Infect 2020; 26:942.e1-942.e5. [DOI: 10.1016/j.cmi.2019.11.012] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2019] [Revised: 11/07/2019] [Accepted: 11/09/2019] [Indexed: 12/14/2022]
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12
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Buscail L, Bournet B, Cordelier P. Role of oncogenic KRAS in the diagnosis, prognosis and treatment of pancreatic cancer. Nat Rev Gastroenterol Hepatol 2020; 17:153-168. [PMID: 32005945 DOI: 10.1038/s41575-019-0245-4] [Citation(s) in RCA: 381] [Impact Index Per Article: 95.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 11/21/2019] [Indexed: 02/08/2023]
Abstract
Pancreatic ductal adenocarcinoma (PDAC) is predicted to be the second most common cause of death within the next 10 years. The prognosis for this disease is poor despite diagnostic progress and new chemotherapeutic regimens. The oncogenic KRAS mutation is the major event in pancreatic cancer; it confers permanent activation of the KRAS protein, which acts as a molecular switch to activate various intracellular signalling pathways and transcription factors inducing cell proliferation, migration, transformation and survival. Several laboratory methods have been developed to detect KRAS mutations in biological samples, including digital droplet PCR (which displays high sensitivity). Clinical studies have revealed that a KRAS mutation assay in fine-needle aspiration material combined with cytopathology increases the sensitivity, accuracy and negative predictive value of cytopathology for a positive diagnosis of pancreatic cancer. In addition, the presence of KRAS mutations in serum and plasma (liquid biopsies) correlates with a worse prognosis. The presence of mutated KRAS can also have therapeutic implications, whether at the gene level per se, during its post-translational maturation, interaction with nucleotides and after activation of the various oncogenic signals. Further pharmacokinetic and toxicological studies on new molecules are required, especially small synthetic molecules, before they can be used in the therapeutic arsenal for pancreatic ductal adenocarcinoma.
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Affiliation(s)
- Louis Buscail
- Department of Gastroenterology, University of Toulouse III, Rangueil Hospital, Toulouse, France. .,INSERM UMR 1037, Toulouse Centre for Cancer Research, University of Toulouse III, Toulouse, France.
| | - Barbara Bournet
- Department of Gastroenterology, University of Toulouse III, Rangueil Hospital, Toulouse, France.,INSERM UMR 1037, Toulouse Centre for Cancer Research, University of Toulouse III, Toulouse, France
| | - Pierre Cordelier
- INSERM UMR 1037, Toulouse Centre for Cancer Research, University of Toulouse III, Toulouse, France
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13
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Santos C, Azuara D, Viéitez JM, Páez D, Falcó E, Élez E, López-López C, Valladares M, Robles-Díaz L, García-Alfonso P, Bugés C, Durán G, Salud A, Navarro V, Capellá G, Aranda E, Salazar R. Phase II study of high-sensitivity genotyping of KRAS, NRAS, BRAF and PIK3CA to ultra-select metastatic colorectal cancer patients for panitumumab plus FOLFIRI: the ULTRA trial. Ann Oncol 2019; 30:796-803. [PMID: 30840064 DOI: 10.1093/annonc/mdz082] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND Several studies show the importance of accurately quantifying not only KRAS and other low-abundant mutations because benefits of anti-EGFR therapies may depend on certain sensitivity thresholds. We assessed whether ultra-selection of patients using a high-sensitive digital PCR (dPCR) to determine KRAS, NRAS, BRAF and PIK3CA status can improve clinical outcomes of panitumumab plus FOLFIRI. PATIENTS AND METHODS This was a single-arm phase II trial that analysed 38 KRAS, NRAS, BRAF and PIK3CA hotspots in tumour tissues of irinotecan-resistant metastatic colorectal cancer patients who received panitumumab plus FOLFIRI until disease progression or early withdrawal. Mutation profiles were identified by nanofluidic dPCR and correlated with clinical outcomes (ORR, overall response rate; PFS, progression-free survival; OS, overall survival) using cut-offs from 0% to 5%. A quantitative PCR (qPCR) analysis was also performed. RESULTS Seventy-two evaluable patients were enrolled. RAS (KRAS/NRAS) mutations were detected in 23 (32%) patients and RAS/BRAF mutations in 25 (35%) by dPCR, while they were detected in 7 (10%) and 11 (15%) patients, respectively, by qPCR. PIK3CA mutations were not considered in the analyses as they were only detected in 2 (3%) patients by dPCR and in 1 (1%) patient by qPCR. The use of different dPCR cut-offs for RAS (KRAS/NRAS) and RAS/BRAF analyses translated into differential clinical outcomes. The highest ORR, PFS and OS in wild-type patients with their lowest values in patients with mutations were achieved with a 5% cut-off. We observed similar outcomes in RAS/BRAF wild-type and mutant patients defined by qPCR. CONCLUSIONS High-sensitive dPCR accurately identified patients with KRAS, NRAS, BRAF and PIK3CA mutations. The optimal RAS/BRAF mutational cut-off for outcome prediction is 5%, which explains that the predictive performance of qPCR was not improved by dPCR. The biological and clinical implications of low-frequent mutated alleles warrant further investigations. CLINICALTRIALS.GOV NUMBER NCT01704703. EUDRACT NUMBER 2012-001955-38.
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Affiliation(s)
- C Santos
- Translational Research Laboratory, Institut Català d'Oncologia Oncobell Program-IDIBELL, L'Hospitalet de Llobregat; Department of Medical Oncology, Institut Català d'Oncologia Oncobell Program-IDIBELL, CIBERONC, L'Hospitalet de Llobregat
| | - D Azuara
- Translational Research Laboratory, Institut Català d'Oncologia Oncobell Program-IDIBELL, L'Hospitalet de Llobregat
| | - J M Viéitez
- Department of Medical Oncology, Hospital Universitario Central de Asturias, Oviedo
| | - D Páez
- Department of Medical Oncology, Hospital de la Santa Creu i Sant Pau, Barcelona
| | - E Falcó
- Department of Medical Oncology, Hospital Son Llàtzer, Palma de Mallorca
| | - E Élez
- Department of Medical Oncology, Hospital Vall d'Hebrón, Barcelona
| | - C López-López
- Department of Medical Oncology, Hospital Universitario Marqués de Valdecilla, Santander
| | - M Valladares
- Department of Medical Oncology, Hospital Universitario de A Coruña, A Coruña
| | - L Robles-Díaz
- Department of Medical Oncology, Hospital Universitario 12 de Octubre, Madrid
| | - P García-Alfonso
- Department of Medical Oncology, Hospital General Universitario Gregorio Marañón, Madrid
| | - C Bugés
- Department of Medical Oncology, Institut Català d'Oncologia-Hospital Germans Trias i Pujol, Badalona, Institut Català d'Oncologia-Hospital Germans Trias i Pujol
| | - G Durán
- Department of Medical Oncology, Hospital Universitario Virgen de la Victoria, Málaga
| | - A Salud
- Department of Medical Oncology, Hospital Universitari Arnau de Vilanova, Lleida
| | - V Navarro
- Clinical Research Unit, Institut Català d'Oncologia, L'Hospitalet de Llobregat
| | - G Capellá
- Translational Research Laboratory, Institut Català d'Oncologia Oncobell Program-IDIBELL, L'Hospitalet de Llobregat
| | - E Aranda
- Department of Medical Oncology, IMIBIC, Hospital Universitario Reina Sofía, Universidad de Córdoba, CIBERONC, Córdoba, Spain
| | - R Salazar
- Translational Research Laboratory, Institut Català d'Oncologia Oncobell Program-IDIBELL, L'Hospitalet de Llobregat; Department of Medical Oncology, Institut Català d'Oncologia Oncobell Program-IDIBELL, CIBERONC, L'Hospitalet de Llobregat.
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14
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Ferchichi M, Jouini R, Koubaa W, Khanchel F, Helal I, Hadad D, Bibani N, Chadli-Debbiche A, BenBrahim E. Ampullary and pancreatic adenocarcinoma-a comparative study. J Gastrointest Oncol 2019; 10:270-275. [PMID: 31032094 DOI: 10.21037/jgo.2018.09.09] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Background Pancreatic ductal adenocarcinoma (PDAC) and ampullary adenocarcinoma (AAC) are 2 gastrointestinal cancers that share overlapping symptoms. Although some studies have proposed the hypothesis of differences in pathogenesis and prognosis in these 2 cancers; they remain treated similarly. The classification of AAC into three subtypes [pancreatobiliary (PB), intestinal (IT) and mixed (M)] is especially crucial for the 3 axes of patients management (diagnosis, prognosis and therapy). Some studies suggest that PB subtype pathogenesis is comparable to PDAC. The objective of this study was to conduct a comparative analysis between PDAC and AAC; notably PB subtype; via mutational status analysis of 3 oncogenes (KRAS, NRAS and BRAF) hoping to consolidate AAC biology understanding. Methods Nine hot spot mutation sites of KRAS, NRAS and BRAF were analysed using pyrosequencing in 39 PDAC and 21 AAC from Tunisian patients. Comparative study was performed using SPSS software. Results Mutations in oncogenes were detected in almost 43% of AAC, especially in PB (47%) and 95% of PDAC. KRAS was the most mutated oncogene. There were statistical significant differences between PDAC and AAC in tumor differentiation (P<0.001), perineural invasion (P<0.001), vascular emboli (P=0.001), T stage (P=0.007), N stage (P=0.001) and mutational status (P<0.001). When comparing PDAC and PB subtype, there were also significant differences in tumor size (P=0.001), tumor differentiation (P<0.001), perineural invasion (P<0.001), vascular emboli (P=0.001), T stage (P=0.033), N stage (P<0.001) and mutational status (P<0.001). Conclusions AAC even PB subtype is different from PDAC. We think that these different tumor types require highly individualized therapy guided by their histomolecular characteristics and that we should stop diagnosing and treating them as a unique entity.
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Affiliation(s)
- Marwa Ferchichi
- University of Sciences, Farhat Hached Campus, Tunis El Manar, Tunis, Tunisia.,Pathology Department, Habib Thameur Hospital, University of Medicine, Tunis, Tunisia
| | - Raja Jouini
- Pathology Department, Habib Thameur Hospital, University of Medicine, Tunis, Tunisia
| | - Wafa Koubaa
- Pathology Department, Habib Thameur Hospital, University of Medicine, Tunis, Tunisia
| | - Fatma Khanchel
- Pathology Department, Habib Thameur Hospital, University of Medicine, Tunis, Tunisia
| | - Imen Helal
- Pathology Department, Habib Thameur Hospital, University of Medicine, Tunis, Tunisia
| | - Dhafer Hadad
- Surgery Department, Habib Thameur Hospital, Tunis, Tunisia
| | - Norsaf Bibani
- Gastroenterology Department, Habib Thameur Hospital, Tunis, Tunisia
| | | | - Ehsen BenBrahim
- Pathology Department, Habib Thameur Hospital, University of Medicine, Tunis, Tunisia
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15
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Dong L, Wang S, Fu B, Wang J. Evaluation of droplet digital PCR and next generation sequencing for characterizing DNA reference material for KRAS mutation detection. Sci Rep 2018; 8:9650. [PMID: 30504843 PMCID: PMC6269532 DOI: 10.1038/s41598-018-27368-3] [Citation(s) in RCA: 68] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2017] [Accepted: 05/23/2018] [Indexed: 01/05/2023] Open
Abstract
KRAS gene mutations are predictive markers of non-response to anti-epidermal growth factor receptor. An increasing number of techniques are being developed to detect KRAS mutations. To obtain consistent and comparable results, a traceable reference material (RM) is necessary for validation the routinely used method. However, a lack of reference methods is a main impediment for deriving traceability and measurement comparability. In this study, droplet digital PCR (ddPCR) and next generation sequencing (NGS) were evaluated. No cross- reactivity was detected with any of the probe by ddPCR. The measured fraction of KRAS mutant allele by ddPCR and NGS agreed with the prepared value by gravimetrical dilution (concordance (k) >0.95 and >0.93 for ddPCR and NGS, respectively). The reliable limit of quantification (LOQ) was 0.1% and 1% for ddPCR and NGS, respectively. In conclusion, the validated ddPCR and NGS are suitable to characterize the KRAS RM due to the high specificity and accuracy. Verification of the LOD of three commercial kits by using the NIM-KRAS-8 RM showed that the LOD was inconsistent with the claimed LOD of the kits (1%) for some assays. This indicates a traceable RM was important for setting up the criteria regarding the LOD for the commercial kit.
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Affiliation(s)
- Lianhua Dong
- National Institute of Metrology, Beijing, 100013, P. R. China.
| | - Shangjun Wang
- Nanjing Institute of Measurement and Testing Technology, Nanjing, 210049, P. R. China
| | - Boqiang Fu
- National Institute of Metrology, Beijing, 100013, P. R. China
| | - Jing Wang
- National Institute of Metrology, Beijing, 100013, P. R. China
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16
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Wu J, Dong M, Santos S, Rigatto C, Liu Y, Lin F. Lab-on-a-Chip Platforms for Detection of Cardiovascular Disease and Cancer Biomarkers. SENSORS 2017; 17:s17122934. [PMID: 29258216 PMCID: PMC5751502 DOI: 10.3390/s17122934] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/28/2017] [Revised: 11/30/2017] [Accepted: 12/13/2017] [Indexed: 12/17/2022]
Abstract
Cardiovascular disease (CVD) and cancer are two leading causes of death worldwide. CVD and cancer share risk factors such as obesity and diabetes mellitus and have common diagnostic biomarkers such as interleukin-6 and C-reactive protein. Thus, timely and accurate diagnosis of these two correlated diseases is of high interest to both the research and healthcare communities. Most conventional methods for CVD and cancer biomarker detection such as microwell plate-based immunoassay and polymerase chain reaction often suffer from high costs, low test speeds, and complicated procedures. Recently, lab-on-a-chip (LoC)-based platforms have been increasingly developed for CVD and cancer biomarker sensing and analysis using various molecular and cell-based diagnostic biomarkers. These new platforms not only enable better sample preparation, chemical manipulation and reaction, high-throughput and portability, but also provide attractive features such as label-free detection and improved sensitivity due to the integration of various novel detection techniques. These features effectively improve the diagnostic test speed and simplify the detection procedure. In addition, microfluidic cell assays and organ-on-chip models offer new potential approaches for CVD and cancer diagnosis. Here we provide a mini-review focusing on recent development of LoC-based methods for CVD and cancer diagnostic biomarker measurements, and our perspectives of the challenges, opportunities and future directions.
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Affiliation(s)
- Jiandong Wu
- Department of Physics and Astronomy, University of Manitoba, Winnipeg, MB, R3T 2N2, Canada.
| | - Meili Dong
- Department of Physics and Astronomy, University of Manitoba, Winnipeg, MB, R3T 2N2, Canada.
- Institute of Applied Technology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei 230088, China.
| | - Susy Santos
- Victoria General Hospital and River Heights/Fort Garry Community Areas, Winnipeg, MB, R3T 2E8, Canada.
| | | | - Yong Liu
- Institute of Applied Technology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei 230088, China.
| | - Francis Lin
- Department of Physics and Astronomy, University of Manitoba, Winnipeg, MB, R3T 2N2, Canada.
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17
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Olmedillas-López S, Lévano-Linares DC, Alexandre CLA, Vega-Clemente L, Sánchez EL, Villagrasa A, Ruíz-Tovar J, García-Arranz M, García-Olmo D. Detection of KRAS G12D in colorectal cancer stool by droplet digital PCR. World J Gastroenterol 2017; 23:7087-7097. [PMID: 29093617 PMCID: PMC5656456 DOI: 10.3748/wjg.v23.i39.7087] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/27/2017] [Revised: 09/15/2017] [Accepted: 09/26/2017] [Indexed: 02/06/2023] Open
Abstract
AIM To assess KRAS G12D mutation detection by droplet digital PCR (ddPCR) in stool-derived DNA from colorectal cancer (CRC) patients.
METHODS In this study, tumor tissue and stool samples were collected from 70 patients with stage I-IV CRC diagnosed by preoperative biopsy. KRAS mutational status was determined by pyrosequencing analysis of DNA obtained from formalin-fixed paraffin-embedded (FFPE) tumor tissues. The KRAS G12D mutation was then analyzed by ddPCR in FFPE tumors and stool-derived DNA from patients with this point mutation. Wild-type (WT) tumors, as determined by pyrosequencing, were included as controls; analysis of FFPE tissue and stool-derived DNA by ddPCR was performed for these patients as well.
RESULTS Among the total 70 patients included, KRAS mutations were detected by pyrosequencing in 32 (45.71%), whereas 38 (54.29%) had WT tumors. The frequency of KRAS mutations was higher in left-sided tumors (11 located in the right colon, 15 in the left, and 6 in the rectum). The predominant point mutation was KRAS G12D (14.29%, n = 10), which was more frequent in early-stage tumors (I-IIA, n = 7). In agreement with pyrosequencing results, the KRAS G12D mutation was detected by ddPCR in FFPE tumor-derived DNA, and only a residual number of mutated copies was found in WT controls. The KRAS G12D mutation was also detected in stool-derived DNA in 80% of all fecal samples from CRC patients with this point mutation.
CONCLUSION ddPCR is a reliable and sensitive method to analyze KRAS G12D mutation in stool-derived DNA from CRC patients, especially at early stages. This non-invasive approach is potentially applicable to other relevant biomarkers for CRC management.
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Affiliation(s)
- Susana Olmedillas-López
- Foundation Health Research Institute-Fundación Jiménez Díaz University Hospital, Madrid 28040, Spain
| | - Dennis César Lévano-Linares
- Department of Surgery, School of Medicine, Universidad Autónoma de Madrid, Madrid 28029, Spain
- Department of Surgery, Rey Juan Carlos University Hospital, Madrid 28933, Spain
| | | | - Luz Vega-Clemente
- Foundation Health Research Institute-Fundación Jiménez Díaz University Hospital, Madrid 28040, Spain
| | - Edurne León Sánchez
- Department of Biomedicine and Biotechnology, Universidad de Alcalá, Madrid 28805, Spain
| | - Alejandro Villagrasa
- Foundation Health Research Institute-Fundación Jiménez Díaz University Hospital, Madrid 28040, Spain
| | - Jaime Ruíz-Tovar
- Department of Surgery, Rey Juan Carlos University Hospital, Madrid 28933, Spain
| | - Mariano García-Arranz
- Foundation Health Research Institute-Fundación Jiménez Díaz University Hospital, Madrid 28040, Spain
- Department of Surgery, School of Medicine, Universidad Autónoma de Madrid, Madrid 28029, Spain
| | - Damián García-Olmo
- Foundation Health Research Institute-Fundación Jiménez Díaz University Hospital, Madrid 28040, Spain
- Department of Surgery, School of Medicine, Universidad Autónoma de Madrid, Madrid 28029, Spain
- Department of Surgery, Fundación Jiménez Díaz University Hospital, Madrid 28040, Spain
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18
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Diagnostic value of CA19.9, circulating tumour DNA and circulating tumour cells in patients with solid pancreatic tumours. Br J Cancer 2017; 117:1017-1025. [PMID: 28772284 PMCID: PMC5625666 DOI: 10.1038/bjc.2017.250] [Citation(s) in RCA: 77] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2017] [Revised: 06/22/2017] [Accepted: 07/05/2017] [Indexed: 12/15/2022] Open
Abstract
Background: The direct comparison of CA19.9, circulating tumour cells (CTCs) and circulating tumour DNA (ctDNA) using endoscopic ultrasound-guided fine needle aspiration (EUS-FNA) has never been performed for the diagnosis of solid pancreatic tumours (SPTs). Methods: We included 68 patients with a SPT referred for EUS-FNA. CTCs were analysed using size-based platform and ctDNA using digital PCR. The sensitivity, specificity, negative and positive predictive values were evaluated for each marker and their combination. Results: SPTs corresponded to 58 malignant tumours (52 pancreatic adenocarcinoma (PA) and 6 others) and 10 benign lesions. The sensitivity and specificity for PA diagnosis were 73% and 88% for EUS-FNA, 67% and 80% for CTC, 65% and 75% for ctDNA and 79% and 93% for CA19.9, respectively. The positivity of at least 2 markers was associated with a sensitivity and specificity of 78% and 91%, respectively. CtDNA was the only marker associated with overall survival (median 5.2 months for ctDNA+ vs 11.0 months for ctDNA−, P=0.01). Conclusions: CA19.9 alone and in combination with ctDNA and/or CTC analysis may represent an efficient method for diagnosing PA in patients with SPTs. Further studies including a larger cohort of patients with both malignant and benign lesions will be necessary to confirm these promising results.
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19
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Gausachs M, Borras E, Chang K, Gonzalez S, Azuara D, Delgado Amador A, Lopez-Doriga A, San Lucas FA, Sanjuan X, Paules MJ, Taggart MW, Davies GE, Ehli EA, Fowler J, Moreno V, Pineda M, You YN, Lynch PM, Lazaro C, Navin NE, Scheet PA, Hawk ET, Capella G, Vilar E. Mutational Heterogeneity in APC and KRAS Arises at the Crypt Level and Leads to Polyclonality in Early Colorectal Tumorigenesis. Clin Cancer Res 2017. [PMID: 28645942 DOI: 10.1158/1078-0432.ccr-17-0821] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Purpose: The majority of genomic alterations causing intratumoral heterogeneity (ITH) in colorectal cancer are thought to arise during early stages of carcinogenesis as a burst but only after truncal mutations in APC have expanded a single founder clone. We have investigated if the initial source of ITH is consequent to multiple independent lineages derived from different crypts harboring distinct truncal APC and driver KRAS mutations, thus challenging the prevailing monoclonal monocryptal model.Experimental Design: High-depth next-generation sequencing and SNP arrays were performed in whole-lesion extracts of 37 familial adenomatous polyposis colorectal adenomas. Also, ultrasensitive genotyping of hotspot mutations of APC and KRAS was performed using nanofluidic PCRs in matched bulk biopsies (n = 59) and crypts (n = 591) from 18 adenomas and seven carcinomas and adjacent normal tissues.Results: Multiple co-occurring truncal APC and driver KRAS alterations were uncovered in whole-lesion extracts from adenomas and subsequently confirmed to belong to multiple clones. Ultrasensitive genotyping of bulk biopsies and crypts revealed novel undetected APC mutations that were prominent among carcinomas, whereas abundant wild-type APC crypts were detected in adenomas. KRAS mutational heterogeneity within crypts was evident in both adenomas and carcinomas with a higher degree of concordance between biopsy and crypt genotyping in carcinomas. Nonrandom heterogeneity among crypts was also observed.Conclusions: The striking degree of nonrandom intercrypt heterogeneity in truncal and driver gene mutations observed in adenomas and carcinomas is consistent with a polycryptal model derived from multiple independent initiation linages as the source of early ITH in colorectal carcinogenesis. Clin Cancer Res; 23(19); 5936-47. ©2017 AACR.
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Affiliation(s)
- Mireia Gausachs
- Hereditary Cancer Program, Catalan Institute of Oncology (ICO - IDIBELL), L'Hospitalet de Llobregat, Barcelona, Spain
| | - Ester Borras
- Department of Clinical Cancer Prevention, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Kyle Chang
- Department of Clinical Cancer Prevention, The University of Texas MD Anderson Cancer Center, Houston, Texas.,Graduate School of Biomedical Sciences, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Sara Gonzalez
- Hereditary Cancer Program, Catalan Institute of Oncology (ICO - IDIBELL), L'Hospitalet de Llobregat, Barcelona, Spain.,CIBERONC, Instituto de Salud Carlos III, Madrid, Spain
| | - Daniel Azuara
- Hereditary Cancer Program, Catalan Institute of Oncology (ICO - IDIBELL), L'Hospitalet de Llobregat, Barcelona, Spain.,CIBERONC, Instituto de Salud Carlos III, Madrid, Spain
| | - Axel Delgado Amador
- Department of Clinical Cancer Prevention, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Adriana Lopez-Doriga
- Cancer Prevention and Control Program, Catalan Institute of Oncology (ICO-IDIBELL) and CIBERESP, L'Hospitalet de Llobregat, Barcelona, Spain
| | - F Anthony San Lucas
- Department of Epidemiology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Xavier Sanjuan
- Department of Pathology, University Hospital Bellvitge (HUB - IDIBELL), L'Hospitalet de Llobregat, Barcelona, Spain
| | - Maria J Paules
- Department of Pathology, University Hospital Bellvitge (HUB - IDIBELL), L'Hospitalet de Llobregat, Barcelona, Spain
| | - Melissa W Taggart
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Gareth E Davies
- Avera Institute for Human Genetics, Sioux Falls, South Dakota
| | - Erik A Ehli
- Avera Institute for Human Genetics, Sioux Falls, South Dakota
| | - Jerry Fowler
- Department of Epidemiology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Victor Moreno
- Cancer Prevention and Control Program, Catalan Institute of Oncology (ICO-IDIBELL) and CIBERESP, L'Hospitalet de Llobregat, Barcelona, Spain.,Department of Clinical Sciences, Medical School, University of Barcelona, Barcelona, Spain
| | - Marta Pineda
- Hereditary Cancer Program, Catalan Institute of Oncology (ICO - IDIBELL), L'Hospitalet de Llobregat, Barcelona, Spain.,CIBERONC, Instituto de Salud Carlos III, Madrid, Spain
| | - Y Nancy You
- Department of Surgical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas.,Clinical Cancer Genetics Program, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Patrick M Lynch
- Clinical Cancer Genetics Program, The University of Texas MD Anderson Cancer Center, Houston, Texas.,Department of Gastroenterology, Hepatology and Nutrition, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Conxi Lazaro
- Hereditary Cancer Program, Catalan Institute of Oncology (ICO - IDIBELL), L'Hospitalet de Llobregat, Barcelona, Spain.,CIBERONC, Instituto de Salud Carlos III, Madrid, Spain
| | - Nicholas E Navin
- Graduate School of Biomedical Sciences, The University of Texas MD Anderson Cancer Center, Houston, Texas.,Department of Genetics, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Paul A Scheet
- Graduate School of Biomedical Sciences, The University of Texas MD Anderson Cancer Center, Houston, Texas.,Department of Epidemiology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Ernest T Hawk
- Department of Clinical Cancer Prevention, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Gabriel Capella
- Hereditary Cancer Program, Catalan Institute of Oncology (ICO - IDIBELL), L'Hospitalet de Llobregat, Barcelona, Spain. .,CIBERONC, Instituto de Salud Carlos III, Madrid, Spain
| | - Eduardo Vilar
- Department of Clinical Cancer Prevention, The University of Texas MD Anderson Cancer Center, Houston, Texas. .,Graduate School of Biomedical Sciences, The University of Texas MD Anderson Cancer Center, Houston, Texas.,Clinical Cancer Genetics Program, The University of Texas MD Anderson Cancer Center, Houston, Texas.,Department of GI Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
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20
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Santos C, Azuara D, Garcia-Carbonero R, Alfonso PG, Carrato A, Elez ME, Gomez A, Losa F, Montagut C, Massuti B, Navarro V, Varela M, Lopez-Doriga A, Moreno V, Valladares M, Manzano JL, Vieitez JM, Aranda E, Sanjuan X, Tabernero J, Capella G, Salazar R. Optimization of RAS/BRAF Mutational Analysis Confirms Improvement in Patient Selection for Clinical Benefit to Anti-EGFR Treatment in Metastatic Colorectal Cancer. Mol Cancer Ther 2017. [DOI: 10.1158/1535-7163.mct-17-0153] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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21
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22
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Abstract
In the last 20 years, improvements in metastatic colorectal cancer treatment lead to a radical raise of outcomes with median survival reaching now more than 30 months. Despite that, the identification of predictive and/or prognostic biomarker still represents a challenging issue, and until today, although clinician and researchers might face with a deeper knowledge of biological mechanisms related to colorectal cancer, many pieces of evidence underline the heterogeneity and the dynamism of such disease. In the present review, we describe the road leading to the discovery of RAS mutations, BRAF V600E mutation, and microsatellite instability role in colorectal cancer; second, we discuss some of the possible major pitfalls of biomarker research, and lastly, we give new suggestions for future research in this field.
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23
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Sho S, Court CM, Kim S, Braxton DR, Hou S, Muthusamy VR, Watson RR, Sedarat A, Tseng HR, Tomlinson JS. Digital PCR Improves Mutation Analysis in Pancreas Fine Needle Aspiration Biopsy Specimens. PLoS One 2017; 12:e0170897. [PMID: 28125707 PMCID: PMC5268428 DOI: 10.1371/journal.pone.0170897] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2016] [Accepted: 01/11/2017] [Indexed: 12/27/2022] Open
Abstract
Applications of precision oncology strategies rely on accurate tumor genotyping from clinically available specimens. Fine needle aspirations (FNA) are frequently obtained in cancer management and often represent the only source of tumor tissues for patients with metastatic or locally advanced diseases. However, FNAs obtained from pancreas ductal adenocarcinoma (PDAC) are often limited in cellularity and/or tumor cell purity, precluding accurate tumor genotyping in many cases. Digital PCR (dPCR) is a technology with exceptional sensitivity and low DNA template requirement, characteristics that are necessary for analyzing PDAC FNA samples. In the current study, we sought to evaluate dPCR as a mutation analysis tool for pancreas FNA specimens. To this end, we analyzed alterations in the KRAS gene in pancreas FNAs using dPCR. The sensitivity of dPCR mutation analysis was first determined using serial dilution cell spiking studies. Single-cell laser-microdissection (LMD) was then utilized to identify the minimal number of tumor cells needed for mutation detection. Lastly, dPCR mutation analysis was performed on 44 pancreas FNAs (34 formalin-fixed paraffin-embedded (FFPE) and 10 fresh (non-fixed)), including samples highly limited in cellularity (100 cells) and tumor cell purity (1%). We found dPCR to detect mutations with allele frequencies as low as 0.17%. Additionally, a single tumor cell could be detected within an abundance of normal cells. Using clinical FNA samples, dPCR mutation analysis was successful in all preoperative FNA biopsies tested, and its accuracy was confirmed via comparison with resected tumor specimens. Moreover, dPCR revealed additional KRAS mutations representing minor subclones within a tumor that were not detected by the current clinical gold standard method of Sanger sequencing. In conclusion, dPCR performs sensitive and accurate mutation analysis in pancreas FNAs, detecting not only the dominant mutation subtype, but also the additional rare mutation subtypes representing tumor heterogeneity.
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Affiliation(s)
- Shonan Sho
- Department of Surgery, University of California Los Angeles, Los Angeles, California, United States of America
- Department of Surgery, Greater Los Angeles Veteran’s Affairs Administration, Los Angeles, California, United States of America
- * E-mail:
| | - Colin M. Court
- Department of Surgery, University of California Los Angeles, Los Angeles, California, United States of America
- Department of Surgery, Greater Los Angeles Veteran’s Affairs Administration, Los Angeles, California, United States of America
- Department of Molecular and Medical Pharmacology, University of California Los Angeles, Los Angeles, California, United States of America
| | - Stephen Kim
- UCLA Center for Pancreatic Diseases, University of California Los Angeles, Los Angeles, California, United States of America
- Division of Digestive Diseases, David Geffen School of Medicine at the University of California Los Angeles, Los Angeles, California, United States of America
| | - David R. Braxton
- Department of Pathology, University of California Los Angeles, Los Angeles, California, United States of America
| | - Shuang Hou
- Department of Molecular and Medical Pharmacology, University of California Los Angeles, Los Angeles, California, United States of America
| | - V. Raman Muthusamy
- UCLA Center for Pancreatic Diseases, University of California Los Angeles, Los Angeles, California, United States of America
- Division of Digestive Diseases, David Geffen School of Medicine at the University of California Los Angeles, Los Angeles, California, United States of America
| | - Rabindra R. Watson
- UCLA Center for Pancreatic Diseases, University of California Los Angeles, Los Angeles, California, United States of America
- Division of Digestive Diseases, David Geffen School of Medicine at the University of California Los Angeles, Los Angeles, California, United States of America
| | - Alireza Sedarat
- UCLA Center for Pancreatic Diseases, University of California Los Angeles, Los Angeles, California, United States of America
- Division of Digestive Diseases, David Geffen School of Medicine at the University of California Los Angeles, Los Angeles, California, United States of America
| | - Hsian-Rong Tseng
- Department of Molecular and Medical Pharmacology, University of California Los Angeles, Los Angeles, California, United States of America
| | - James S. Tomlinson
- Department of Surgery, University of California Los Angeles, Los Angeles, California, United States of America
- Department of Surgery, Greater Los Angeles Veteran’s Affairs Administration, Los Angeles, California, United States of America
- UCLA Center for Pancreatic Diseases, University of California Los Angeles, Los Angeles, California, United States of America
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24
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Ahrberg CD, Manz A, Chung BG. Polymerase chain reaction in microfluidic devices. LAB ON A CHIP 2016; 16:3866-3884. [PMID: 27713993 DOI: 10.1039/c6lc00984k] [Citation(s) in RCA: 138] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
The invention of the polymerase chain reaction (PCR) has caused a revolution in molecular biology, giving access to a method of amplifying deoxyribonucleic acid (DNA) molecules across several orders of magnitude. Since the first application of PCR in a microfluidic device was developed in 1998, an increasing number of researchers have continued the development of microfluidic PCR systems. In this review, we introduce recent developments in microfluidic-based space and time domain devices as well as discuss various designs integrated with multiple functions for sample preparation and detection. The development of isothermal nucleic acid amplification and digital PCR microfluidic devices within the last five years is also highlighted. Furthermore, we introduce various commercial microfluidic PCR devices.
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Affiliation(s)
| | - Andreas Manz
- Microfluidics group, KIST-Europe, Saarbrücken, Germany and Mechanotronics Department, Universität des Saarlandes, Saarbrücken, Germany
| | - Bong Geun Chung
- Department of Mechanical Engineering, Sogang University, Seoul, Korea.
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25
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Ginesta MM, Diaz-Riascos ZV, Busquets J, Pelaez N, Serrano T, Peinado MÀ, Jorba R, García-Borobia FJ, Capella G, Fabregat J. APC promoter is frequently methylated in pancreatic juice of patients with pancreatic carcinomas or periampullary tumors. Oncol Lett 2016; 12:2210-2216. [PMID: 27602165 DOI: 10.3892/ol.2016.4868] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2015] [Accepted: 05/23/2016] [Indexed: 12/18/2022] Open
Abstract
Early detection of pancreatic and periampullary neoplasms is critical to improve their clinical outcome. The present authors previously demonstrated that DNA hypermethylation of adenomatous polyposis coli (APC), histamine receptor H2 (HRH2), cadherin 13 (CDH13), secreted protein acidic and cysteine rich (SPARC) and engrailed-1 (EN-1) promoters is frequently detected in pancreatic tumor cells. The aim of the present study was to assess their prevalence in pancreatic juice of carcinomas of the pancreas and periampullary area. A total of 135 pancreatic juices obtained from 85 pancreatic cancer (PC), 26 ampullary carcinoma (AC), 10 intraductal papillary mucinous neoplasm (IPMN) and 14 chronic pancreatitis (CP) patients were analyzed. The methylation status of the APC, HRH2, CDH13, SPARC and EN-1 promoters was analyzed using methylation specific-melting curve analysis (MS-MCA). Kirsten rat sarcoma viral oncogene homolog (KRAS) mutations were also tested with allele-specific quantitative polymerase chain reaction amplification. Out of the 5 promoters analyzed, APC (71%) and HRH2 (65%) were the most frequently methylated in PC juice. APC methylation was also detected at a high frequency in AC (76%) and IPMN (80%), but only occasionally observed in CP (7%). APC methylation had a high sensitivity (71-80%) for all types of cancer analyzed. The panel (where a sample scored as positive when ≥2 markers were methylated) did not outperform APC as a single marker. Finally, KRAS detection in pancreatic juice offered a lower sensitivity (50%) and specificity (71%) for detection of any cancer. APC hypermethylation in pancreatic juice, as assessed by MS-MCA, is a frequent event of potential clinical usefulness in the diagnosis of pancreatic and periampullary neoplasms.
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Affiliation(s)
- Mireia M Ginesta
- Translational Research Laboratory, Catalan Institute of Oncology, Bellvitge Biomedical Research Institute, Duran i Reynals Hospital, 08907 Barcelona, Spain
| | - Zamira Vanessa Diaz-Riascos
- Translational Research Laboratory, Catalan Institute of Oncology, Bellvitge Biomedical Research Institute, Duran i Reynals Hospital, 08907 Barcelona, Spain
| | - Juli Busquets
- Department of General and Digestive Surgery, Bellvitge University Hospital, 08907 Barcelona, Spain
| | - Núria Pelaez
- Department of General and Digestive Surgery, Bellvitge University Hospital, 08907 Barcelona, Spain
| | - Teresa Serrano
- Department of Pathology, Bellvitge University Hospital, 08907 Barcelona, Spain
| | - Miquel Àngel Peinado
- Department of Mechanism of Tumor Progression, Institute of Predictive and Personalized Cancer Medicine, 08916 Barcelona, Spain
| | - Rosa Jorba
- Department of Surgery, Joan XXIII Hospital, 43005 Tarragona, Spain
| | | | - Gabriel Capella
- Translational Research Laboratory, Catalan Institute of Oncology, Bellvitge Biomedical Research Institute, Duran i Reynals Hospital, 08907 Barcelona, Spain
| | - Joan Fabregat
- Department of General and Digestive Surgery, Bellvitge University Hospital, 08907 Barcelona, Spain
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26
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Iwama E, Takayama K, Harada T, Okamoto I, Ookubo F, Kishimoto J, Baba E, Oda Y, Nakanishi Y. Highly sensitive and quantitative evaluation of the EGFR T790M mutation by nanofluidic digital PCR. Oncotarget 2016; 6:20466-73. [PMID: 26015401 PMCID: PMC4653018 DOI: 10.18632/oncotarget.4058] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2015] [Accepted: 04/20/2015] [Indexed: 12/27/2022] Open
Abstract
The mutation of T790M in EGFR is a major mechanism of resistance to treatment with EGFR-TKIs. Only qualitative detection (presence or absence) of T790M has been described to date, however. Digital PCR (dPCR) analysis has recently been applied to the quantitative detection of target molecules in cancer with high sensitivity. In the present study, 25 tumor samples (13 obtained before and 12 after EGFR-TKI treatment) from 18 NSCLC patients with activating EGFR mutations were evaluated for T790M with dPCR. The ratio of the number of T790M alleles to that of activating mutation alleles (T/A) was determined. dPCR detected T790M in all 25 samples. Although T790M was present in all pre-TKI samples from 13 patients, 10 of these patients had a low T/A ratio and manifested substantial tumor shrinkage during treatment with EGFR-TKIs. In six of seven patients for whom both pre- and post-TKI samples were available, the T/A ratio increased markedly during EGFR-TKI treatment. Highly sensitive dPCR thus detected T790M in all NSCLC patients harboring activating EGFR mutations whether or not they had received EGFR-TKI treatment. Not only highly sensitive but also quantitative detection of T790M is important for evaluation of the contribution of T790M to EGFR-TKI resistance.
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Affiliation(s)
- Eiji Iwama
- Faculty of Medical Sciences, Department of Comprehensive Clinical Oncology, Kyushu University, Fukuoka, Japan.,Research Institute for Diseases of the Chest, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Koichi Takayama
- Research Institute for Diseases of the Chest, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Taishi Harada
- Research Institute for Diseases of the Chest, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Isamu Okamoto
- Center for Clinical and Translational Research, Kyushu University Hospital, Fukuoka, Japan
| | - Fumihiko Ookubo
- Division of Diagnostic Pathology, Kyushu University Hospital, Fukuoka, Japan
| | - Junji Kishimoto
- Department of Research and Development of Next Generation Medicine, Kyushu University, Fukuoka, Japan
| | - Eishi Baba
- Faculty of Medical Sciences, Department of Comprehensive Clinical Oncology, Kyushu University, Fukuoka, Japan
| | - Yoshinao Oda
- Department of Anatomic Pathology, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Yoichi Nakanishi
- Research Institute for Diseases of the Chest, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan.,Center for Clinical and Translational Research, Kyushu University Hospital, Fukuoka, Japan
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Van Krieken JHJM, Rouleau E, Ligtenberg MJL, Normanno N, Patterson SD, Jung A. RAS testing in metastatic colorectal cancer: advances in Europe. Virchows Arch 2016; 468:383-96. [PMID: 26573425 PMCID: PMC4830882 DOI: 10.1007/s00428-015-1876-7] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2015] [Revised: 10/20/2015] [Accepted: 10/22/2015] [Indexed: 12/22/2022]
Abstract
Personalized medicine shows promise for maximizing efficacy and minimizing toxicity of anti-cancer treatment. KRAS exon 2 mutations are predictive of resistance to epidermal growth factor receptor-directed monoclonal antibodies in patients with metastatic colorectal cancer. Recent studies have shown that broader RAS testing (KRAS and NRAS) is needed to select patients for treatment. While Sanger sequencing is still used, approaches based on various methodologies are available. Few CE-approved kits, however, detect the full spectrum of RAS mutations. More recently, "next-generation" sequencing has been developed for research use, including parallel semiconductor sequencing and reversible termination. These techniques have high technical sensitivities for detecting mutations, although the ideal threshold is currently unknown. Finally, liquid biopsy has the potential to become an additional tool to assess tumor-derived DNA. For accurate and timely RAS testing, appropriate sampling and prompt delivery of material is critical. Processes to ensure efficient turnaround from sample request to RAS evaluation must be implemented so that patients receive the most appropriate treatment. Given the variety of methodologies, external quality assurance programs are important to ensure a high standard of RAS testing. Here, we review technical and practical aspects of RAS testing for pathologists working with metastatic colorectal cancer tumor samples. The extension of markers from KRAS to RAS testing is the new paradigm for biomarker testing in colorectal cancer.
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Affiliation(s)
- J Han J M Van Krieken
- Department of Pathology, Radboud University Medical Center, P.O. Box 9101, 6500 HB, Nijmegen, Netherlands.
| | | | - Marjolijn J L Ligtenberg
- Department of Pathology, Radboud University Medical Center, P.O. Box 9101, 6500 HB, Nijmegen, Netherlands
| | - Nicola Normanno
- Cell Biology and Biotherapy Unit, INT-Fondazione Pascale, Naples, Italy
| | - Scott D Patterson
- Amgen Inc., Thousand Oaks, CA, USA
- Gilead Sciences, Inc., Foster City, CA, USA
| | - Andreas Jung
- Institute of Pathology, University of Munich, Munich, Germany
- German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
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28
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Azuara D, Santos C, Lopez-Doriga A, Grasselli J, Nadal M, Sanjuan X, Marin F, Vidal J, Montal R, Moreno V, Bellosillo B, Argiles G, Elez E, Dienstmann R, Montagut C, Tabernero J, Capellá G, Salazar R. Nanofluidic Digital PCR and Extended Genotyping of RAS and BRAF for Improved Selection of Metastatic Colorectal Cancer Patients for Anti-EGFR Therapies. Mol Cancer Ther 2016; 15:1106-12. [PMID: 27037411 DOI: 10.1158/1535-7163.mct-15-0820] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2015] [Accepted: 02/17/2016] [Indexed: 11/16/2022]
Abstract
The clinical significance of low-frequent RAS pathway-mutated alleles and the optimal sensitivity cutoff value in the prediction of response to anti-EGFR therapy in metastatic colorectal cancer (mCRC) patients remains controversial. We aimed to evaluate the added value of genotyping an extended RAS panel using a robust nanofluidic digital PCR (dPCR) approach. A panel of 34 hotspots, including RAS (KRAS and NRAS exons 2/3/4) and BRAF (V600E), was analyzed in tumor FFPE samples from 102 mCRC patients treated with anti-EGFR therapy. dPCR was compared with conventional quantitative PCR (qPCR). Response rates, progression-free survival (PFS), and overall survival (OS) were correlated to the mutational status and the mutated allele fraction. Tumor response evaluations were not available in 9 patients and were excluded for response rate analysis. Twenty-two percent of patients were positive for one mutation with qPCR (mutated alleles ranged from 2.1% to 66.6%). Analysis by dPCR increased the number of positive patients to 47%. Mutated alleles for patients only detected by dPCR ranged from 0.04% to 10.8%. An inverse correlation between the fraction of mutated alleles and radiologic response was observed. ROC analysis showed that a fraction of 1% or higher of any mutated alleles offered the best predictive value for all combinations of RAS and BRAF analysis. In addition, this threshold also optimized prediction both PFS and OS. We conclude that mutation testing using an extended gene panel, including RAS and BRAF with a threshold of 1% improved prediction of response to anti-EGFR therapy. Mol Cancer Ther; 15(5); 1106-12. ©2016 AACR.
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Affiliation(s)
- Daniel Azuara
- Translational Research Laboratory, Catalan Insitute of Oncology (ICO), Bellvitge Biomedical Research Institute (IDIBELL), L'Hospitalet de Llobregat, Barcelona, Spain
| | - Cristina Santos
- Translational Research Laboratory, Catalan Insitute of Oncology (ICO), Bellvitge Biomedical Research Institute (IDIBELL), L'Hospitalet de Llobregat, Barcelona, Spain. Department of Medical Oncology, Catalan Insitute of Oncology (ICO), Bellvitge Biomedical Research Institute (IDIBELL), L'Hospitalet de Llobregat, Barcelona, Spain
| | - Adriana Lopez-Doriga
- Unit of Biomarkers and Susceptibility, Catalan Insitute of Oncology (ICO), Bellvitge Biomedical Research Institute (IDIBELL), L'Hospitalet de Llobregat, Barcelona, Spain
| | - Julieta Grasselli
- Department of Medical Oncology, Catalan Insitute of Oncology (ICO), Bellvitge Biomedical Research Institute (IDIBELL), L'Hospitalet de Llobregat, Barcelona, Spain. Department of Medical Oncology, Vall d'Hebron University Hospital and Institute of Oncology (VHIO), Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Marga Nadal
- Translational Research Laboratory, Catalan Insitute of Oncology (ICO), Bellvitge Biomedical Research Institute (IDIBELL), L'Hospitalet de Llobregat, Barcelona, Spain
| | - Xavier Sanjuan
- Department of Pathology, University Hospital Bellvitge (HUB-IDIBELL), L'Hospitalet de Llobregat, Barcelona, Spain
| | - Fátima Marin
- Translational Research Laboratory, Catalan Insitute of Oncology (ICO), Bellvitge Biomedical Research Institute (IDIBELL), L'Hospitalet de Llobregat, Barcelona, Spain
| | - Joana Vidal
- Department of Medical Oncology, Hospital Universitari del Mar, Barcelona, Spain
| | - Robert Montal
- Department of Medical Oncology, Catalan Insitute of Oncology (ICO), Bellvitge Biomedical Research Institute (IDIBELL), L'Hospitalet de Llobregat, Barcelona, Spain
| | - Victor Moreno
- Unit of Biomarkers and Susceptibility, Catalan Insitute of Oncology (ICO), Bellvitge Biomedical Research Institute (IDIBELL), L'Hospitalet de Llobregat, Barcelona, Spain
| | - Beatriz Bellosillo
- Department of Pathology, Hospital Universitari del Mar, Barcelona, Spain
| | - Guillem Argiles
- Department of Medical Oncology, Vall d'Hebron University Hospital and Institute of Oncology (VHIO), Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Elena Elez
- Department of Medical Oncology, Vall d'Hebron University Hospital and Institute of Oncology (VHIO), Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Rodrigo Dienstmann
- Department of Medical Oncology, Vall d'Hebron University Hospital and Institute of Oncology (VHIO), Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Clara Montagut
- Department of Medical Oncology, Hospital Universitari del Mar, Barcelona, Spain
| | - Josep Tabernero
- Department of Medical Oncology, Vall d'Hebron University Hospital and Institute of Oncology (VHIO), Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Gabriel Capellá
- Translational Research Laboratory, Catalan Insitute of Oncology (ICO), Bellvitge Biomedical Research Institute (IDIBELL), L'Hospitalet de Llobregat, Barcelona, Spain.
| | - Ramon Salazar
- Translational Research Laboratory, Catalan Insitute of Oncology (ICO), Bellvitge Biomedical Research Institute (IDIBELL), L'Hospitalet de Llobregat, Barcelona, Spain. Department of Medical Oncology, Catalan Insitute of Oncology (ICO), Bellvitge Biomedical Research Institute (IDIBELL), L'Hospitalet de Llobregat, Barcelona, Spain.
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Olmedillas López S, García-Olmo DC, García-Arranz M, Guadalajara H, Pastor C, García-Olmo D. KRAS G12V Mutation Detection by Droplet Digital PCR in Circulating Cell-Free DNA of Colorectal Cancer Patients. Int J Mol Sci 2016; 17:484. [PMID: 27043547 PMCID: PMC4848940 DOI: 10.3390/ijms17040484] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2016] [Revised: 03/21/2016] [Accepted: 03/24/2016] [Indexed: 12/14/2022] Open
Abstract
KRAS mutations are responsible for resistance to anti-epidermal growth factor receptor (EGFR) therapy in colorectal cancer patients. These mutations sometimes appear once treatment has started. Detection of KRAS mutations in circulating cell-free DNA in plasma (“liquid biopsy”) by droplet digital PCR (ddPCR) has emerged as a very sensitive and promising alternative to serial biopsies for disease monitoring. In this study, KRAS G12V mutation was analyzed by ddPCR in plasma DNA from 10 colorectal cancer patients and compared to six healthy donors. The percentage of KRAS G12V mutation relative to wild-type sequences in tumor-derived DNA was also determined. KRAS G12V mutation circulating in plasma was detected in 9 of 10 colorectal cancer patients whose tumors were also mutated. Colorectal cancer patients had 35.62 copies of mutated KRAS/mL plasma, whereas in healthy controls only residual copies were found (0.62 copies/mL, p = 0.0066). Interestingly, patients with metastatic disease showed a significantly higher number of mutant copies than M0 patients (126.25 versus 9.37 copies/mL, p = 0.0286). Wild-type KRAS was also significantly elevated in colorectal cancer patients compared to healthy controls (7718.8 versus 481.25 copies/mL, p = 0.0002). In conclusion, KRAS G12V mutation is detectable in plasma of colorectal cancer patients by ddPCR and could be used as a non-invasive biomarker.
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Affiliation(s)
- Susana Olmedillas López
- Health Research Institute-Fundación Jiménez Díaz University Hospital (IIS-FJD), Madrid 28040, Spain.
| | - Dolores C García-Olmo
- Experimental Research Unit, General University Hospital of Albacete, Albacete 02006, Spain.
| | - Mariano García-Arranz
- Health Research Institute-Fundación Jiménez Díaz University Hospital (IIS-FJD), Madrid 28040, Spain.
- Department of Surgery, School of Medicine, Autónoma University of Madrid, Madrid 28029, Spain.
| | - Héctor Guadalajara
- Department of Surgery, School of Medicine, Autónoma University of Madrid, Madrid 28029, Spain.
- Department of General Surgery, General Hospital of Villalba, Madrid 28400, Spain.
| | - Carlos Pastor
- Department of Surgery, Fundación Jiménez Díaz University Hospital, Madrid 28040, Spain.
| | - Damián García-Olmo
- Health Research Institute-Fundación Jiménez Díaz University Hospital (IIS-FJD), Madrid 28040, Spain.
- Department of Surgery, School of Medicine, Autónoma University of Madrid, Madrid 28029, Spain.
- Department of Surgery, Fundación Jiménez Díaz University Hospital, Madrid 28040, Spain.
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30
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Raub CB, Lee CC, Shibata D, Taylor C, Kartalov E. HistoMosaic Detecting KRAS G12V Mutation Across Colorectal Cancer Tissue Slices through in Situ PCR. Anal Chem 2016; 88:2792-8. [PMID: 26820161 PMCID: PMC7446286 DOI: 10.1021/acs.analchem.5b04460] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
We report on HistoMosaic, a novel technique for genetic analysis of formalin-fixed, paraffin-embedded tissue slices. It combines microfluidic compartmentalization, in situ allele-specific PCR, and fluorescence microscopy. The experimental proof of principle was achieved by in situ detection of KRAS G12V mutation in colorectal cancer tissues and is presented herein. HistoMosaic offers the ability to detect mutations over the entire tissue slide simultaneously, rapidly, economically, and without selection bias, while coregistering the genetic information with the preserved morphological information. Thus, HistoMosaic has wide applicability in basic science as a tool to map genetic heterogeneity. It is also a platform to build companion diagnostics for targeted therapies in oncology, to help ensure that the right drug is given to the right patient, thereby saving healthcare resources and improving patient outcomes.
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Affiliation(s)
| | - Chen-Chung Lee
- Department of Pathology, Keck School of Medicine of the University of Southern California, 2011 Zonal Avenue, Los Angeles, California 90089, United States
| | - Darryl Shibata
- Department of Pathology, Keck School of Medicine of the University of Southern California, 2011 Zonal Avenue, Los Angeles, California 90089, United States
| | - Clive Taylor
- Department of Pathology, Keck School of Medicine of the University of Southern California, 2011 Zonal Avenue, Los Angeles, California 90089, United States
| | - Emil Kartalov
- Department of Pathology, Keck School of Medicine of the University of Southern California, 2011 Zonal Avenue, Los Angeles, California 90089, United States
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31
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Abstract
Digital PCR is a robust PCR technique that enables precise and accurate absolute quantitation of target molecules by diluting and partitioning of the samples into numerous compartments. Automated partitioning can be attained by creating "water-in-oil" emulsion (emulsion-based digital PCR) or using a chip with microchannels (microfluidics-based digital PCR). We discuss the advantages and a wide variety of clinical applications of this technique. We describe the droplet digital RT-PCR protocol published by Jennings et al. for identification and absolute quantitation of BCR-ABL1 transcripts.
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A Non-Invasive Droplet Digital PCR (ddPCR) Assay to Detect Paternal CFTR Mutations in the Cell-Free Fetal DNA (cffDNA) of Three Pregnancies at Risk of Cystic Fibrosis via Compound Heterozygosity. PLoS One 2015; 10:e0142729. [PMID: 26561302 PMCID: PMC4641687 DOI: 10.1371/journal.pone.0142729] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2015] [Accepted: 10/26/2015] [Indexed: 12/12/2022] Open
Abstract
Introduction Non-invasive prenatal diagnosis (NIPD) makes use of cell-free fetal DNA (cffDNA) in the mother’s bloodstream as an alternative to invasive sampling methods such as amniocentesis or CVS, which carry a 0.5–1% risk of fetal loss. We describe a droplet digital PCR (ddPCR) assay designed to inform the testing options for couples whose offspring are at risk of suffering from cystic fibrosis via compound heterozygosity. By detecting the presence or absence of the paternal mutation in the cffDNA, it is possible to predict whether the fetus will be an unaffected carrier (absence) or whether further invasive testing is indicated (presence). Methods We selected a family in which the parents were known to carry different mutated CFTR alleles as our test system. NIPD was performed for three of their pregnancies during the first trimester (at around 11–12 weeks of gestation). Taqman probes were designed against an amplicon in exon 11 of the CFTR gene, to quantify the proportion of mutant (ΔF508-MUT; FAM) and normal (ΔF508-NOR; VIC) alleles at position c.1521_1523 of the CFTR gene. Discussion The assay correctly and unambiguously recognized the ΔF508-MUT CFTR allele in the cffDNA of all three proband fetuses and none of the six unaffected control fetuses. In conclusion, the Bio-Rad QX100 was found to be a cost-effective and technically undemanding platform for designing bespoke NIPD assays.
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Zhang BO, Xu CW, Shao Y, Wang HT, Wu YF, Song YY, Li XB, Zhang Z, Wang WJ, Li LQ, Cai CL. Comparison of droplet digital PCR and conventional quantitative PCR for measuring EGFR gene mutation. Exp Ther Med 2015; 9:1383-1388. [PMID: 25780439 PMCID: PMC4353752 DOI: 10.3892/etm.2015.2221] [Citation(s) in RCA: 70] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2014] [Accepted: 12/19/2014] [Indexed: 02/02/2023] Open
Abstract
Early detection of epidermal growth factor receptor (EGFR) mutation, particularly EGFR T790M mutation, is of clinical significance. The aim of the present study was to compare the performances of amplification refractory mutation system-based quantitative polymerase chain reaction (ARMS-qPCR) and droplet digital polymerase chain reaction (ddPCR) approaches in the detection of EGFR mutation and explore the feasibility of using ddPCR in the detection of samples with low mutation rates. EGFR gene mutations in plasmid samples with different T790M mutation rates (0.1-5%) and 10 clinical samples were detected using the ARMS-qPCR and ddPCR approaches. The results demonstrated that the ARMS-qPCR method stably detected the plasmid samples (6,000 copies) with 5 and 1% mutation rates, while the ddPCR approach reliably detected those with 5% (398 copies), 1% (57 copies), 0.5% (24 copies) and 0.1% (average 6 copies) mutation rates. For the 10 clinical samples, the results for nine samples by the ARMS-qPCR and ddPCR methods were consistent; however, the sample N006, indicated to be EGFR wild-type by ARMS-qPCR, was revealed to have a clear EGFR T790M mutation with seven copies of mutant alleles in a background of 6,000 wild-type copies using ddPCR technology. This study demonstrates the feasibility of applying the ddPCR system to detect EGFR mutation and identified the advantage of ddPCR in the detection of samples with a low EGFR mutation abundance, particularly the secondary EGFR T790M resistance mutation, which enables early diagnosis before acquired resistance to tyrosine kinase inhibitors becomes clinically detectable.
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Affiliation(s)
- B O Zhang
- Department of Pathology, Affiliated Hospital of Academy of Military Medical Sciences, Beijing 100071, P.R. China
| | - Chun-Wei Xu
- Department of Pathology, Affiliated Hospital of Academy of Military Medical Sciences, Beijing 100071, P.R. China
| | - Yun Shao
- Department of Pathology, Affiliated Hospital of Academy of Military Medical Sciences, Beijing 100071, P.R. China
| | - Huai-Tao Wang
- Department of Pathology, Affiliated Hospital of Academy of Military Medical Sciences, Beijing 100071, P.R. China
| | - Yong-Fang Wu
- Department of Pathology, Affiliated Hospital of Academy of Military Medical Sciences, Beijing 100071, P.R. China
| | - Ye-Ying Song
- Department of Pathology, Affiliated Hospital of Academy of Military Medical Sciences, Beijing 100071, P.R. China
| | - Xiao-Bing Li
- Department of Pathology, Affiliated Hospital of Academy of Military Medical Sciences, Beijing 100071, P.R. China
| | - Zhe Zhang
- Wuhan YZY Medical Science and Technology Co., Ltd., Wuhan, Hubei 430075, P.R. China
| | - Wen-Jing Wang
- Wuhan YZY Medical Science and Technology Co., Ltd., Wuhan, Hubei 430075, P.R. China
| | - Li-Qiong Li
- Wuhan YZY Medical Science and Technology Co., Ltd., Wuhan, Hubei 430075, P.R. China
| | - Cong-Li Cai
- Wuhan YZY Medical Science and Technology Co., Ltd., Wuhan, Hubei 430075, P.R. China
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Development and validation of a 48-target analytical method for high-throughput monitoring of genetically modified organisms. Sci Rep 2015; 5:7616. [PMID: 25556930 PMCID: PMC5154595 DOI: 10.1038/srep07616] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2014] [Accepted: 12/03/2014] [Indexed: 12/12/2022] Open
Abstract
The rapid increase in the number of genetically modified (GM) varieties has led to a demand for high-throughput methods to detect genetically modified organisms (GMOs). We describe a new dynamic array-based high throughput method to simultaneously detect 48 targets in 48 samples on a Fludigm system. The test targets included species-specific genes, common screening elements, most of the Chinese-approved GM events, and several unapproved events. The 48 TaqMan assays successfully amplified products from both single-event samples and complex samples with a GMO DNA amount of 0.05 ng, and displayed high specificity. To improve the sensitivity of detection, a preamplification step for 48 pooled targets was added to enrich the amount of template before performing dynamic chip assays. This dynamic chip-based method allowed the synchronous high-throughput detection of multiple targets in multiple samples. Thus, it represents an efficient, qualitative method for GMO multi-detection.
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35
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Abstract
Activating mutation of KRAS plays a significant role in the pathogenesis of common human malignancies and molecular testing of KRAS mutation has emerged as an essential biomarker in the current practice of clinical oncology. The presence of KRAS mutation is generally associated with clinical aggressiveness of the cancer and reduced survival of the patient. Therapeutically, KRAS mutation testing has maximum utility in stratifying metastatic colorectal carcinoma and lung cancer patients for treatment with targeted therapy. Diagnostically, KRAS mutation testing is useful in the workup of pancreaticobiliary and thyroid cancers, particularly using cytological specimens. In the era of precision medicine, the role of KRAS mutation testing is poised to expand, likely in a setting of combinatorial therapeutic strategy and requiring additional mutation testing of its upstream and/or downstream effectors.
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Affiliation(s)
- Sudhir Perincheri
- Department of Pathology, Yale University School of Medicine, 310 Cedar Street, New Haven, CT 06520-8023, USA
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Jia Y, Sanchez JA, Wangh LJ. Kinetic hairpin oligonucleotide blockers for selective amplification of rare mutations. Sci Rep 2014; 4:5921. [PMID: 25082368 PMCID: PMC4118197 DOI: 10.1038/srep05921] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2014] [Accepted: 07/15/2014] [Indexed: 01/13/2023] Open
Abstract
Detection of rare mutant alleles in an excess of wild type alleles is increasingly important in cancer diagnosis. Several methods for selective amplification of a mutant allele via the polymerase chain reaction (PCR) have been reported, but each of these methods has its own limitations. A common problem is that Taq DNA polymerase errors early during amplification generate false positive mutations which also accumulate exponentially. In this paper, we described a novel method using hairpin oligonucleotide blockers that can selectively inhibit the amplification of wild type DNA during LATE-PCR amplification. LATE-PCR generates double-stranded DNA exponentially followed by linear amplification of single-stranded DNA. The efficiency of the blocker is optimized by adjusting the LATE-PCR temperature cycling profile. We also demonstrate that it is possible to minimize false positive signals caused by Taq DNA polymerase errors by using a mismatched excess primer plus a modified PCR profile to preferentially enrich for mutant target sequences prior to the start of the exponential phase of LATE-PCR amplification. In combination these procedures permit amplification of specific KRAS mutations in the presence of more than 10,000 fold excess of wild type DNA without false positive signals.
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Affiliation(s)
- Yanwei Jia
- 1] Department of Biology, Brandeis University, Waltham, MA 02453, USA [2] State Key Laboratory of Analog and Mixed-Signal VLSI, University of Macau, Macau, China
| | | | - Lawrence J Wangh
- Department of Biology, Brandeis University, Waltham, MA 02453, USA
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37
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Kinz E, Leiherer A, Lang AH, Drexel H, Muendlein A. Accurate quantitation of JAK2 V617F allele burden by array-based digital PCR. Int J Lab Hematol 2014; 37:217-24. [DOI: 10.1111/ijlh.12269] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2014] [Accepted: 05/12/2014] [Indexed: 02/02/2023]
Affiliation(s)
- E. Kinz
- Vorarlberg Institute for Vascular Investigation and Treatment (VIVIT); Feldkirch Austria
- Private University of the Principality of Liechtenstein; Triesen Liechtenstein
| | - A. Leiherer
- Vorarlberg Institute for Vascular Investigation and Treatment (VIVIT); Feldkirch Austria
- Private University of the Principality of Liechtenstein; Triesen Liechtenstein
| | - A. H. Lang
- Vorarlberg Institute for Vascular Investigation and Treatment (VIVIT); Feldkirch Austria
- Department of Medicine and Cardiology; Academic Teaching Hospital Feldkirch; Feldkirch Austria
| | - H. Drexel
- Vorarlberg Institute for Vascular Investigation and Treatment (VIVIT); Feldkirch Austria
- Private University of the Principality of Liechtenstein; Triesen Liechtenstein
- Department of Medicine and Cardiology; Academic Teaching Hospital Feldkirch; Feldkirch Austria
- Drexel College University of Medicine; Philadelphia PA USA
| | - A. Muendlein
- Vorarlberg Institute for Vascular Investigation and Treatment (VIVIT); Feldkirch Austria
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Castillejo A, Vargas G, Castillejo MI, Navarro M, Barberá VM, González S, Hernández-Illán E, Brunet J, Ramón y Cajal T, Balmaña J, Oltra S, Iglesias S, Velasco A, Solanes A, Campos O, Sánchez Heras AB, Gallego J, Carrasco E, González Juan D, Segura A, Chirivella I, Juan MJ, Tena I, Lázaro C, Blanco I, Pineda M, Capellá G, Soto JL. Prevalence of germline MUTYH mutations among Lynch-like syndrome patients. Eur J Cancer 2014; 50:2241-50. [PMID: 24953332 DOI: 10.1016/j.ejca.2014.05.022] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2014] [Revised: 04/17/2014] [Accepted: 05/22/2014] [Indexed: 01/04/2023]
Abstract
BACKGROUND AND AIMS Individuals with tumours showing mismatch repair (MMR) deficiency not linked to germline mutations or somatic methylation of MMR genes have been recently referred as having 'Lynch-like syndrome' (LLS). The genetic basis of these LLS cases is unknown. MUTYH-associated polyposis patients show some phenotypic similarities to Lynch syndrome patients. The aim of this study was to investigate the prevalence of germline MUTYH mutations in a large series of LLS patients. METHODS Two hundred and twenty-five probands fulfilling LLS criteria were included in this study. Screening of MUTYH recurrent mutations, whole coding sequencing and a large rearrangement analysis were undertaken. Age, sex, clinical, pathological and molecular characteristics of tumours including KRAS mutations were assessed. RESULTS We found a prevalence of 3.1% of MAP syndrome in the whole series of LLS (7/225) and 3.9% when only cases fulfilling clinical criteria were considered (7/178). Patients with MUTYH biallelic mutations had more adenomas than monoallelic (P=0.02) and wildtype patients (P<0.0001). Six out of nine analysed tumours from six biallelic MUTYH carriers harboured KRAS-p.G12C mutation. This mutation was found to be associated with biallelic MUTYH germline mutation when compared with reported series of unselected colorectal cancer cohorts (P<0.0001). CONCLUSIONS A proportion of unexplained LLS cases is caused by biallelic MUTYH mutations. The obtained results further justify the inclusion of MUTYH in the diagnostic strategy for Lynch syndrome-suspected patients.
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Affiliation(s)
- Adela Castillejo
- Molecular Genetics Laboratory, Elche University Hospital, Elche, Alicante, Spain
| | - Gardenia Vargas
- Hereditary Cancer Program, Catalan Institute of Oncology, ICO-IDIBELL, Hospitalet de Llobregat, Barcelona, Spain
| | | | - Matilde Navarro
- Hereditary Cancer Program, Catalan Institute of Oncology, ICO-IDIBELL, Hospitalet de Llobregat, Barcelona, Spain
| | | | - Sara González
- Hereditary Cancer Program, Catalan Institute of Oncology, ICO-IDIBELL, Hospitalet de Llobregat, Barcelona, Spain
| | | | - Joan Brunet
- Hereditary Cancer Program, Catalan Institute of Oncology, ICO-IdIBGI, Girona, Spain
| | | | | | - Silvestre Oltra
- Genetics Department, La Fe University Hospital, Valencia, Spain
| | - Sílvia Iglesias
- Hereditary Cancer Program, Catalan Institute of Oncology, ICO-IDIBELL, Hospitalet de Llobregat, Barcelona, Spain
| | - Angela Velasco
- Hereditary Cancer Program, Catalan Institute of Oncology, ICO-IdIBGI, Girona, Spain
| | - Ares Solanes
- Hereditary Cancer Program, Catalan Institute of Oncology, Badalona, Barcelona, Spain
| | - Olga Campos
- Hereditary Cancer Program, Catalan Institute of Oncology, ICO-IDIBELL, Hospitalet de Llobregat, Barcelona, Spain
| | - Ana Beatriz Sánchez Heras
- Genetic Counselling in Cancer, Hereditary Cancer Program, Elche University Hospital, Elche, Alicante, Spain; Department of Medical Oncology, Elche University Hospital, Elche, Alicante, Spain
| | - Javier Gallego
- Department of Medical Oncology, Elche University Hospital, Elche, Alicante, Spain
| | | | | | - Angel Segura
- Genetic Counselling in Cancer, Hereditary Cancer Program, La Fe University Hospital, Valencia, Spain
| | - Isabel Chirivella
- Genetic Counselling in Cancer, Hereditary Cancer Program, Clinical University Hospital of Valencia, Valencia, Spain
| | - María José Juan
- Genetic Counselling in Cancer, Hereditary Cancer Program, Valencian Institute of Oncology, Valencia, Spain
| | - Isabel Tena
- Genetic Counselling in Cancer, Hereditary Cancer Program, Provincial Hospital of Castellón, Castellón, Spain
| | - Conxi Lázaro
- Hereditary Cancer Program, Catalan Institute of Oncology, ICO-IDIBELL, Hospitalet de Llobregat, Barcelona, Spain
| | - Ignacio Blanco
- Hereditary Cancer Program, Catalan Institute of Oncology, ICO-IDIBELL, Hospitalet de Llobregat, Barcelona, Spain; Hereditary Cancer Program, Catalan Institute of Oncology, Badalona, Barcelona, Spain
| | - Marta Pineda
- Hereditary Cancer Program, Catalan Institute of Oncology, ICO-IDIBELL, Hospitalet de Llobregat, Barcelona, Spain
| | - Gabriel Capellá
- Hereditary Cancer Program, Catalan Institute of Oncology, ICO-IDIBELL, Hospitalet de Llobregat, Barcelona, Spain
| | - José Luis Soto
- Molecular Genetics Laboratory, Elche University Hospital, Elche, Alicante, Spain.
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Barrett AN, Chitty LS. Developing noninvasive diagnosis for single-gene disorders: the role of digital PCR. Methods Mol Biol 2014; 1160:215-228. [PMID: 24740232 DOI: 10.1007/978-1-4939-0733-5_17] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Cell-free fetal DNA constitutes approximately 10 % of the cell-free DNA found in maternal plasma and can be used as a reliable source of fetal genetic material for noninvasive prenatal diagnosis (NIPD) from early pregnancy. The relatively high levels of maternal background can make detection of paternally inherited point mutations challenging. Diagnosis of inheritance of autosomal recessive disorders using qPCR is even more challenging due to the high background of mutant maternal allele. Digital PCR is a very sensitive modified method of quantitative real-time PCR (qPCR), allowing absolute quantitation and rare allele detection without the need for standards or normalization. Samples are diluted and then partitioned into a large number of small qPCR reactions, some of which contain the target molecule and some which do not; the proportion of positive reactions can be used to calculate the concentration of targets in the initial sample. Here we discuss the use of digital PCR as an accurate approach to NIPD for single-gene disorders.
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Affiliation(s)
- Angela N Barrett
- Department of Obstetrics and Gynaecology, Yong Loo Lin School of Medicine, National University of Singapore, NUHS Tower Block, Level 12, 1E Kent Ridge Road, Singapore, 119228, Singapore,
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Hagemann IS, Cottrell CE, Lockwood CM. Design of targeted, capture-based, next generation sequencing tests for precision cancer therapy. Cancer Genet 2013; 206:420-31. [DOI: 10.1016/j.cancergen.2013.11.003] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2013] [Revised: 11/12/2013] [Accepted: 11/18/2013] [Indexed: 12/15/2022]
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Taira C, Matsuda K, Yamaguchi A, Sueki A, Koeda H, Takagi F, Kobayashi Y, Sugano M, Honda T. Novel high-speed droplet-allele specific-polymerase chain reaction: application in the rapid genotyping of single nucleotide polymorphisms. Clin Chim Acta 2013; 424:39-46. [PMID: 23685227 DOI: 10.1016/j.cca.2013.04.024] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2013] [Accepted: 04/23/2013] [Indexed: 11/29/2022]
Abstract
BACKGROUND Single nucleotide alterations such as single nucleotide polymorphisms (SNP) and single nucleotide mutations are associated with responses to drugs and predisposition to several diseases, and they contribute to the pathogenesis of malignancies. We developed a rapid genotyping assay based on the allele-specific polymerase chain reaction (AS-PCR) with our droplet-PCR machine (droplet-AS-PCR). METHODS Using 8 SNP loci, we evaluated the specificity and sensitivity of droplet-AS-PCR. Buccal cells were pretreated with proteinase K and subjected directly to the droplet-AS-PCR without DNA extraction. The genotypes determined using the droplet-AS-PCR were then compared with those obtained by direct sequencing. RESULTS Specific PCR amplifications for the 8 SNP loci were detected, and the detection limit of the droplet-AS-PCR was found to be 0.1-5.0% by dilution experiments. Droplet-AS-PCR provided specific amplification when using buccal cells, and all the genotypes determined within 9 min were consistent with those obtained by direct sequencing. CONCLUSIONS Our novel droplet-AS-PCR assay enabled high-speed amplification retaining specificity and sensitivity and provided ultra-rapid genotyping. Crude samples such as buccal cells were available for the droplet-AS-PCR assay, resulting in the reduction of the total analysis time. Droplet-AS-PCR may therefore be useful for genotyping or the detection of single nucleotide alterations.
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Affiliation(s)
- Chiaki Taira
- Department of Laboratory Medicine, Shinshu University Hospital, 3-1-1 Asahi, Matsumoto 390-8621, Japan
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Quantitative microfluidic biomolecular analysis for systems biology and medicine. Anal Bioanal Chem 2013; 405:5743-58. [PMID: 23568613 DOI: 10.1007/s00216-013-6930-1] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2013] [Revised: 03/10/2013] [Accepted: 03/19/2013] [Indexed: 12/12/2022]
Abstract
In the postgenome era, biology and medicine are rapidly evolving towards quantitative and systems studies of complex biological systems. Emerging breakthroughs in microfluidic technologies and innovative applications are transforming systems biology by offering new capabilities to address the challenges in many areas, such as single-cell genomics, gene regulation networks, and pathology. In this review, we focus on recent progress in microfluidic technology from the perspective of its applications to promoting quantitative and systems biomolecular analysis in biology and medicine.
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Straub T, Baird C, Bartholomew RA, Colburn H, Seiner D, Victry K, Zhang L, Bruckner-Lea CJ. Estimated copy number of Bacillus anthracis plasmids pXO1 and pXO2 using digital PCR. J Microbiol Methods 2012; 92:9-10. [PMID: 23142659 DOI: 10.1016/j.mimet.2012.10.013] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2012] [Revised: 10/23/2012] [Accepted: 10/29/2012] [Indexed: 10/27/2022]
Abstract
We evaluated digital PCR (dPCR) to directly enumerate plasmid and chromosome copies in three strains of Bacillus anthracis. Copy number estimates based on conventional quantitative PCR (qPCR) highlighted the variability of using qPCR to measure copy number whereas estimates based on direct sequencing are comparable to dPCR.
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Affiliation(s)
- Timothy Straub
- Chemical and Biological Signature Sciences Group, National Security Directorate, Pacific Northwest National Laboratory, Richland, WA 99354, United States.
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